Metadata-Version: 2.1
Name: pymuster
Version: 0.1.4
Summary: A registration tool for medical images
Home-page: https://github.com/CRAI-OUS/MUSTER
License: MIT
Keywords: registration,medical,MRI,CT,PET,SPECT,non-rigid,deformation
Author: Edvard Grødem
Author-email: edvard.grodem@gmail.com
Requires-Python: >=3.11,<3.13
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: alive-progress (>=3.1.4,<4.0.0)
Requires-Dist: click (>=8.1.7,<9.0.0)
Requires-Dist: numpy (>=1.26.0,<2.0.0)
Requires-Dist: torch (==2.0.0)
Project-URL: Repository, https://github.com/CRAI-OUS/MUSTER
Description-Content-Type: text/markdown

# MUSTER: Multi Session Temporal Registration
**MUSTER** is a robust tool designed for the registration and analysis of longitudinal 3D medical images. Built on PyTorch, MUSTER leverages GPU acceleration for fast and efficient processing. For instance, a timeseries of 8 images at a ``[160, 160, 160]`` resolution can typically be processed in just 2 minutes.

![Divergence and Jacobi Determinant](docs/figures/muster_div_detjac.png)

## Installation
Ensure that Python is installed on your machine. Then execute the following command to install **MUSTER**:

```bash
pip install pymuster
```
## Inctructions
**MUSTER** can be used in two ways, either as a command line tool or as a Python package

### Command Line Interface
TO BE IMPLEMENTED
After installing the package via pip, execute the following command to perform registration:
```bash
muster registration <in_dir> <out_dir>
```
Here ``<in_dir>`` refers to the directory path where your subject's data in BIDS format is stored. Each session should be in its own subfolder. Ensure that the session folders are named in a way that their alphabetical sorting aligns with the correct temporal order.

``<out_dir>`` is the directory where the output will be saved. Deformation data for each session relative to all other sessions will be stored in this directory.

### Python Package
For more flexibility and access to advanced settings, you can also use **MUSTER** as a Python package. Please refer to the in-code documentation for details on how to use it.

